ruvX Resolved · high auto-curated
H37Rv Rv2554c · MTBC0 mtbc0_002722 ·
170 aa · 2896803–2897315 (-) ·
RefSeq NP_217070.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Holliday junction resolvase |
|---|---|
| MTBC0 PGAP re-annotation | Holliday junction resolvase RuvX |
| Revised (this work) | Holliday junction resolvase RuvX. Pfam: RuvX (PF03652.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGV7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative pre-16S rRNA nuclease |
| EC (curated) |
EC 3.1.-.-
|
| Curated function | Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA. |
UniProt still lists this protein as Putative pre-16S rRNA nuclease; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | ruvX |
| eggNOG description | Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA |
| Orthologous group | COG0816 |
| KEGG orthology |
K07447
|
| Gene Ontology (37) |
GO:0000966, GO:0000967, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006364, GO:0006396, GO:0006725, GO:0006807 +25 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RuvX | PF03652.21 | 2.0e-38 | 23–155 | Holliday junction resolvase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: alaS (alanine--tRNA ligase), high confidence from genomic context alone (score 981 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2555c alaS |
alanine--tRNA ligase | 993 | 981 ctx | neighborhood:881 coexpression:826 textmining:652 |
Rv2552c aroE |
shikimate 5-dehydrogenase | 909 | 909 ctx | neighborhood:881 |
Rv2553c mltG |
membrane protein | 908 | 909 ctx | neighborhood:882 |
Rv2551c hyp |
hypothetical protein | 802 | 802 ctx | neighborhood:793 |
Rv2556c hyp |
hypothetical protein | 788 | 789 ctx | neighborhood:779 |
Rv0038 hyp |
hypothetical protein | 741 | 703 | coexpression:678 |
Rv2537c aroD |
3-dehydroquinate dehydratase | 581 | 581 ctx | neighborhood:544 |
Rv2539c aroK |
shikimate kinase | 564 | 565 ctx | neighborhood:544 |
Rv2540c aroF |
chorismate synthase | 560 | 560 ctx | neighborhood:544 |
Rv2727c miaA |
tRNA delta(2)-isopentenylpyrophosphate transferase | 545 | 545 | coexpression:508 |
Rv2557 hyp |
hypothetical protein | 469 | 469 ctx | neighborhood:466 |
Rv2584c apt |
adenine phosphoribosyltransferase | 442 | 443 | coexpression:426 |
Rv1644 tsnR |
23S rRNA methyltransferase TsnR | 438 | 434 | |
Rv3265c wbbL1 |
N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase | 426 | 427 | coexpression:407 |
Rv0510 hemC |
porphobilinogen deaminase | 426 | 426 | coexpression:407 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: Holliday junction resolvase
- MTBC0 PGAP product: Holliday junction resolvase RuvX
- Pfam (hmmscan --cut_ga): RuvX PF03652.21 (E=2e-38)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217070.1)
- Domains: Pfam-A via hmmscan --cut_ga — RuvX (PF03652.21)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0816 - Curated reference: UniProt P9WGV7 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
28 functional partner(s); context anchor
alaS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002722|Rv2554c|ruvX MVPAQHRPPDRPGDPAHDPGRGRRLGIDVGAARIGVACSDPDAILATPVETVRRDRSGKHLRRLAALAAELEAVEVIVGLPRTLADRIGRSAQDAIELAEALARRVSPTPVRLADERLTTVSAQRSLRQAGVRASEQRAVIDQAAAVAILQSWLDERLAAMAGTQEGSDA